Wheat bran leachate (WBL) has been shown to have an inhibitory effect on Microcystis aeruginosa in this study. In order to explore the inhibitory mechanism of WBL on M. aeruginosa, physiological responses of M. aeruginosa NIES-843 under the WBL stress were studied. The expressions of six important genes related to the D1 protein of photosynthetic processes (psbA), synthesis of microcystins (mcyB), antioxidant protein peroxiredoxin (prx), synthesis of fatty acid (fabZ) and the repair of biological macromolecules (recA, grpE) were studied. Under the WBL stress, no significant change was found in expressions of both grpE and recA, but expressions of psbA, fabZ and prx were shown to be down-regulated, and slight up-regulated expression was found in mcyB. It was shown that oxygen evolution of M. aeruginosa NIES-843 was significantly depressed, and intracellular ATP contents became lower, after exposure to WBL. Similarly, maximum electron transport rates of photosynthetic activities decreased significantly, but intracellular reactive oxygen species levels boosted dramatically under the WBL stress, and cell lysis was observed. Therefore, it is suggested that photosynthetic systems and membranes were the potential targets of toxicity of WBL on M. aeruginosa, and the oxidative damage is an important mechanism explaining the inhibitory effect of WBL on M. aeruginosa.